Nanowire-based system for analysis of nucleic acids

1. A method for sequencing a nucleic acid template, the method comprising:

forming a set of nanowire assemblies each including a separate semiconductor nanowire and a different probe covalently bound to the semiconductor nanowire, the semiconductor nanowire connected at a first end to a first electrode and at a second end to a second electrode, a detector connected to the electrodes to detect an electrical characteristic of the semiconductor nanowire;

contacting the set of nanowire assemblies with a template nucleic acid, the template nucleic acid forming nucleic acid duplexes with a plurality of the different probes;

contacting the nucleic acid duplexes with an extension nucleic acid, the extension nucleic acid joined to a probe of the plurality of different probes;

disrupting the nucleic acid duplexes to form single strand nucleic acid; and

measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

2. The method of claim 1 , further comprising contacting the nanowire assembly with a ligase enzyme while contacting the extension nucleic acid.

3. The method of claim 1 , wherein the step of measuring includes a step of measuring substantially no change in the electrical characteristic of a select nanowire assembly, thereby indicating that the extension nucleic acid is not added to an associated probe.

4. The method of claim 1 , wherein the step of measuring determines a change in the electrical characteristic correlating the joining of the extension nucleic acid to the probe.

5. The method of claim 1 , wherein the different probe of includes a region of nucleotide sequence variation in a population.

6. The method of claim 5 , wherein a variation in the region is disposed at or near an end of the different probe.

7. The method of claim 5 , wherein the nucleotide sequence variation corresponds to a polymorphism in a population.

8. The method of claim 1 , wherein a first nucleic acid assembly includes a first probe having a region with a first nucleotide sequence variation and a second nucleic acid assembly includes a second probe having the region with a second nucleotide sequence variation.

9. The method of claim 1 , wherein disrupting includes changing a temperature of the set of nanowire assemblies.

10. The method of claim 1 , wherein disrupting includes adjusting an ionic strength of a solution surrounding the set of nanowire assemblies.

11. The method of claim 1 , wherein disrupting includes changing the concentration of an organic solvent.

12. The method of claim 1 , wherein disrupting includes enzymatically disrupting.

13. The method of claim 1 , wherein disrupting includes changing an electric field of a nucleic acid assembly.

14. A method for sequencing a nucleic acid template, the method comprising:

forming a set of nanowire assemblies each including a separate semiconductor nanowire and a different probe covalently bound to the semiconductor nanowire, the different probe of including a region of nucleotide sequence variation disposed at or near an end of the probe, the nucleotide sequence variation corresponding to a polymorphism in a population, the semiconductor nanowire connected at a first end to a first electrode and at a second end to a second electrode, a detector connected to the electrodes to detect an electrical characteristic of the semiconductor nanowire;

contacting the set of nanowire assemblies with a template nucleic acid, the template nucleic acid forming nucleic acid duplexes with a plurality of the different probes, wherein a first probe is paired at its end with the template nucleic acid and a second probe is unpaired at its end with the template nucleic acid;

contacting the nucleic acid duplexes with an extension nucleic acid and a ligase enzyme, the extension nucleic acid joined to the first probe of the plurality of different probes;

disrupting the nucleic acid duplexes to form single strand nucleic acid; and

measuring an electrical characteristic of a nanowire assembly of the set of nanowire assemblies.

15. The method of claim 14 , wherein the step of measuring includes a step of measuring substantially no change in the electrical characteristic of a nanowire assembly associated with the second probe.

16. The method of claim 14 , wherein the step of measuring determines a change in the electrical characteristic correlating the joining of the extension nucleic acid to the first probe.

17. The method of claim 14 , wherein disrupting includes changing a temperature of the set of nanowire assemblies.

18. The method of claim 14 , wherein disrupting includes adjusting an ionic strength of a solution surrounding the set of nanowire assemblies.

19. The method of claim 14 , wherein disrupting includes changing the concentration of an organic solvent.

20. The method of claim 14 , wherein disrupting includes enzymatically disrupting.